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Time varying harmonics are becoming an increasing issue in power quality analysis. Especially for future all-electric navy ships which will feature closely coupled and complex electrical power systems with a large number of power electronic converter systems. In this paper, real-time hardware-in-the-loop (RT-HIL) simulation is discussed as one of the tools to help analyzing the time varying power quality problems. First, recent additions to extensive RT-HIL capabilities of the Center for Advanced Power System (CAPS) at Florida State University are presented. Subsequently, results form RT-HIL experiments with commercial grade power electronics controllers are discussed.